If I understand the goal correctly you need to create blocks:
$$J(n) = \begin{bmatrix} R(n) \\ R(n+1) \end{bmatrix} $$
(Recall that matrix multiplication is recursive (ex: 4x4 marix is just a 2x2 of 2x2 blocks etc...))
Then the equation $R(n+2) +A_n R(n+1) +B_n R(n) = 0$ can be rewritten as
$$ \begin{bmatrix} R(n+1) \\ R(n+2) \end{bmatrix} + \begin{bmatrix} 0 && -I_n \\ B_n && A_n \end{bmatrix} \begin{bmatrix} R(n) \\ R(n+1) \end{bmatrix} = 0 $$
I.E.
$$ J(n+1) = -\begin{bmatrix} 0 && -I_n \\ B_n && A_n \end{bmatrix} J(n) $$
At this point things get a little harder. You are dealing with the matrix equivalent of say $f(n+1) = n*f(n)$ whereas to use matrix exponentials you want the matrix equivalent of $f(n+1) = 2*f(n)$. The latter being a constant leading to a nice matrix formula but the former being a varying multiple.
I'll have to return to this question but one basically wants to ask two questions to wrap up here:
Given $f(n+1) = P(n) * f(n)$ how does one interpolate the curve itself? (ex finding the gamma function from the factorial relation)
Then how does (1) generalize to the matrix setting?
I'm not sure off the top of my head how to proceed with these. Although for (1) you can probably modify @JM's techniques for the partition function here
The gist of his technique is to to consider $f(x) = \sum_{n=0}^{\infty} P(n) x^n$ and then to evaluate the fractional derivative $\frac{1}{\Gamma({\alpha +1})}\frac{d^{\alpha}}{dx^{\alpha}}[f(x)]_{\text{evaluate at} \ x = 0}$ for a suitable choice of contour to create a curve that interpolates $P(n)$ and is "natural" in a vague sense (JM found considering a sequence of circles approaching radius 1 from 0 to be the natural "interpolater" for the partition function and that might hold for many other functions).
Now we want to put this into the matrix setting. Which can be done by letting $x$ in $f(x)$ above no longer be a complex number but a matrix. The only caveat here is "what is a natural contour in the matrix setting?" and more importantly "is there a natural contour?".
In the event we weren't dealing with shift $J(n+1) = A(n) J(n)$ but a derivative $J' = A(x)J(x)$ then the Time ordered exponential is what you seek. So you are essentially trying to find a "discrete time ordered exponential".
*you mention that $A_n, B_n$ are polynomial. If they were merely linear or even affine functions of $n$ then techniques involving the matrix gamma function might be useful.